Cargo containers (e.g., multi-transportation modality containers used to transport goods via ship, train, or truck, such as intermodal containers also known as shipping containers, sea cans or conex boxes) can present security risks because various unwanted materials can be placed in such containers and there are significant challenges associated with determining the exact contents of inbound containers at a port or other border entry. One of the primary challenges relates to the high number of such containers that arrive daily at busy ports and the need to quickly scan the containers so as not to unduly disrupt the flow of goods at such ports. The detection of special nuclear material (SNM) (i.e., fissile material) is of particular interest, but other unwanted materials may include explosives, drugs, and other contraband.